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Help
ARDEN
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Identifier Index
[
A
B
C
D
E
F
G
H
I
J K
L
M
N
O
P
Q
R
S
T
U V
W
X Y Z
_
]
A
a
(in
script-arden_create
)
algnedToRef
(in
core.AnalyseMapping
)
AnalyseMapping
(in
core
)
aa_dist_seq()
(in
core.ReadAndWrite
)
AlignedReadsdic
(in
core.AnalyseMapping
)
algnedToArt
(in
core.AnalyseMapping
)
alngts
(in
core.AnalyseMapping
)
B
b
(in
script-arden_create
)
bases
(in
script-arden_create
)
build_ORF()
(in
core.FindOrfs
)
C
CalculateRoc2()
(in
core.PlotData
)
core
CreateCompareList()
(in
core.AnalyseMapping
)
CheckForSameAlignments()
(in
core.AnalyseMapping
)
counter1
(in
script-arden_filter
)
createdic()
(in
core.Prep
)
CompareAlignments()
(in
core.AnalyseMapping
)
counter2
(in
script-arden_filter
)
CustomRead
(in
core.AnalyseMapping
)
ComputeRQScore()
(in
core.AnalyseMapping
)
Create()
(in
script-arden_create
)
E
extendReadDic()
(in
core.AnalyseMapping
)
F
filter()
(in
script-arden_filter
)
find_orfs()
(in
core.FindOrfs
)
findstop_help()
(in
core.FindOrfs
)
FilterSAM()
(in
script-arden_filter
)
FindOrfs
(in
core
)
G
genetic_code
(in
core.Prep
)
getHammingdistance()
(in
core.AnalyseMapping
)
getNextLine()
(in
core.AnalyseMapping
)
getAlignmentLength()
(in
core.AnalyseMapping
)
gethammingdistance()
(in
core.ReadAndWrite
)
getNumberOf()
(in
core.AnalyseMapping
)
getAllID()
(in
core.AnalyseMapping
)
getmean()
(in
core.AnalyseMapping
)
GetOrderDictionary()
(in
core.AnalyseMapping
)
GetCompletePath()
(in
core.AnalyseMapping
)
getMisGap()
(in
core.AnalyseMapping
)
getRanks()
(in
core.AnalyseMapping
)
getCustomRead()
(in
core.AnalyseMapping
)
getMisGapRQ()
(in
script-arden_filter
)
getsum()
(in
core.AnalyseMapping
)
getdifference()
(in
core.InsertMutations
)
getMutation()
(in
core.InsertMutations
)
getTPRead()
(in
core.AnalyseMapping
)
I
initOutFiles()
(in
core.AnalyseMapping
)
isContained()
(in
TPRead
)
isvalidposition()
(in
core.InsertMutations
)
InsertMutations
(in
core
)
isSaneAlignment()
(in
core.AnalyseMapping
)
isvalidtriplet()
(in
core.Prep
)
L
loadpickle()
(in
core.AnalyseMapping
)
loadpickle()
(in
core.Prep
)
M
main()
(in
script-arden_analyze
)
mutate_random()
(in
core.InsertMutations
)
N
nucleotide_dist_file()
(in
core.ReadAndWrite
)
nucleotide_dist_seq()
(in
core.ReadAndWrite
)
P
PlotData
(in
core
)
Prep
(in
core
)
plotOverviewHist()
(in
core.PlotData
)
printExample()
(in
script-arden_create
)
R
ReadAndWrite
(in
core
)
readHeader()
(in
script-arden_filter
)
readSAMline()
(in
core.AnalyseMapping
)
ReadArtificialSAMfileHTSeq()
(in
core.AnalyseMapping
)
ReadID
(in
core.AnalyseMapping
)
ReadSAMnoMem()
(in
core.AnalyseMapping
)
readdna()
(in
core.ReadAndWrite
)
readInput()
(in
core.AnalyseMapping
)
returnIndex()
(in
core.AnalyseMapping
)
ReadFromTab()
(in
core.AnalyseMapping
)
readReadQualities()
(in
core.AnalyseMapping
)
returnSequence()
(in
core.AnalyseMapping
)
S
savepickle()
(in
core.AnalyseMapping
)
script-arden_analyze
script-arden_filter
savepickle()
(in
core.Prep
)
script-arden_create
SkipHeader()
(in
core.AnalyseMapping
)
T
TestFiles()
(in
script-arden_analyze
)
toStr()
(in
CustomRead
)
TPRead
(in
core.AnalyseMapping
)
toObjself()
(in
CustomRead
)
toStr()
(in
TPRead
)
trans_seq()
(in
core.Prep
)
toObjself()
(in
TPRead
)
toStrNoMem()
(in
CustomRead
)
trapezoidal_rule()
(in
core.PlotData
)
W
writefile()
(in
core.ReadAndWrite
)
writeoverview()
(in
core.ReadAndWrite
)
writeToTabRef()
(in
core.AnalyseMapping
)
writeFilteredReads()
(in
script-arden_filter
)
writeToTabArt()
(in
core.AnalyseMapping
)
_
__init__()
(in
CustomRead
)
__package__
(in
core.FindOrfs
)
__package__
(in
core.ReadAndWrite
)
__init__()
(in
ReadID
)
__package__
(in
core.InsertMutations
)
__package__
(in
core
)
__init__()
(in
TPRead
)
__package__
(in
core.PlotData
)
__package__
(in
script-arden_analyze
)
__package__
(in
core.AnalyseMapping
)
__package__
(in
core.Prep
)
__package__
(in
script-arden_filter
)
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